EP3S150ES VCC/VCCL Resistance to ground

Are you sure all power supplies to the FPGA are up? There are several that will keep the device in power on reset. if they are not up all the way.

there's also a note on the ramp time of VCCPD and VCCPGM:

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VCCPGM and VCCPD must ramp up from 0 V to the desired voltage level within 100 ms. If

these supplies are not ramped up within this specified time, your Stratix III device

will not configure successfully. If your system does not allow ramp-up time of 100 ms

or less, you must hold nCONFIG low until all power supplies are stable.

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When you are trying to configure it via active serial, are you seeing any activity on the DCLK, DATA0 and CS pins?

Pete